ENST00000687881.1:n.162-11870C>T

Variant names:

• chr12-3935310-G-A
• rs7133541
• ENST00000687881.1:n.162-11870C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000687881.1(ENSG00000288729):​n.162-11870C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.361 in 149,200 control chromosomes in the GnomAD database, including 11,680 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.36 (11680 hom., cov: 31)
• Consequence: ENSG00000288729 ENST00000687881.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38

Genes affected

ENSG00000288729 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369608	XR_931557.4	n.161-11870C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288729	ENST00000687881.1	n.162-11870C>T		intron_variant	Intron 2 of 2
ENSG00000288729	ENST00000690597.1	n.273-11870C>T		intron_variant	Intron 3 of 3
ENSG00000288729	ENST00000701907.1	n.160+21422C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.361 AC: 53853 AN: 149100 Hom.: 11658 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.204

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.392

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.361 AC: 53915 AN: 149200 Hom.: 11680 Cov.: 31 AF XY: 0.363 AC XY: 26433 AN XY: 72794

Gnomad4 AFR AF: 0.432

Gnomad4 AMR AF: 0.372

Gnomad4 ASJ AF: 0.412

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.434

Gnomad4 FIN AF: 0.306

Gnomad4 NFE AF: 0.328

Gnomad4 OTH AF: 0.397

Alfa AF: 0.336 Hom.: 6403

Asia WGS AF: 0.409 AC: 1386 AN: 3406

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.73
DANN	Benign	0.40

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7133541; hg19: chr12-4044476;